All it stipulates is that you will have to live there "a reasonable amount of time" which can vary market to market. 

Apparently, the FHA loan stipulates that the buyer must live in one of the units.

Could we say nothing to the lender, allow month-to-month Tenant B to stay, and then hope that Tenant A voluntarily moves out at the end of his original lease without the lender realizing we failed to meet the 60-day move-in stipulation due to the circumstances?

Your contract should stipulate who pays what fees. 

Are there any stipulations or legality issues if I were to refinance as my primary property and then turn it into a rental?

@Steve,Whoever told you the "until created" thing is not correct.The IRS rules stipulate that you may not produce any direct or indirect benefit between a plan and a disqualified party and a retirement plan.If your personal business is creating opportunities and putting capital and energy into deals that you then take over with your IRA, your business is providing services to your IRA. 

In order to pay off the initial debt, I have considered a few personal and commercial refi options that all require about 25% as a down payment, based on the respective LTV stipulations.

I told her the contract stipulates specifically that I can request an increase and read the verbiage for her..

If the landlord wished to work out a payment plan to accommodate the issues brought on by this emergency than I strongly recommend it be done in a stipulated agreement that comes after the service of an unfiled unlawful detainer.

Another thing to keep in mind is that if you use a VA loan for a different property with fewer units, one of the stipulations of the VA loan is that you are the occupant of that property for the duration of the mortgage, which means that if you decide to move on to your next house hack to grow your portfolio, you would have to refinance your house with a conventional loan.